Two decades before the events of Fire Emblem: The Binding Blade, a traveler collapses in the plains of Sacae in eastern Elibe.
This traveler, a tactician, is discovered by Lyn, daughter of the chieftain of the Lorca tribe, and nursed back to health. Seeing as Lyn has recently lost her parents to bandit attacks, the swordfighter and tactician decide to work together to make things right.
Meanwhile, in the Lycia region that holds sway over southern Elibe, Elbert—the marquess of Pherae and a lord of the Lycian League—mysteriously vanishes. Elbert's son, Eliwood, sets out to find him with the aid of his friend Hector, brother of the marquess of Ostia. Through this journey they come to learn of a conspiracy to unravel the Lycian League, orchestrated by a cabal of assassins called the Black Fang. After rescuing a mysterious pair of siblings from these assassins, Eliwood and his companions find themselves drawn deep into a secretive battle over the power of dragons.

This game is the first to have players taking on the role of army tactician to assist the heroes in their fight.